Promoting, advancing and defending Intelligent Design via data, logic and Intelligent Reasoning and exposing the theory of evolution as the nonsense it is.
I also educate evotards about ID and the theory of evolution one tard at a time and sometimes in groups

Thursday, August 09, 2007

Evidences for Common Design- Evidence 1 the Fundamental Unity

In this series of evidences each evidence presented is independent of any specific (design) mechanism.

Intelligent design is a good explanation for a number of biochemical systems, but I should insert a word of caution. Intelligent design theory has to be seen in context: it does not try to explain everything. We live in a complex world where lots of different things can happen. When deciding how various rocks came to be shaped the way they are a geologist might consider a whole range of factors: rain, wind, the movement of glaciers, the activity of moss and lichens, volcanic action, nuclear explosions, asteroid impact, or the hand of a sculptor. The shape of one rock might have been determined primarily by one mechanism, the shape of another rock by another mechanism.

Similarly, evolutionary biologists have recognized that a number of factors might have affected the development of life: common descent, natural selection, migration, population size, founder effects (effects that may be due to the limited number of organisms that begin a new species), genetic drift (spread of "neutral," nonselective mutations), gene flow (the incorporation of genes into a population from a separate population), linkage (occurrence of two genes on the same chromosome), and much more. The fact that some biochemical systems were designed by an intelligent agent does not mean that any of the other factors are not operative, common, or important. Dr M. Behe

The Fundamental Unity of Living Organisms

Prediction 1.1: The Fundamental Unity of Living Organisms

According to the theory of common design, modern living organisms, with all their incredible differences, are the progeny of one single grand put in motion in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all living organisms. Some of the macroscopic properties that characterize all living organisms are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to sustain a population.

If every living species were ed around these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, a basic prediction of the genealogical relatedness of all life, combined with the constraint of design, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes.

Confirmation:

The common polymers of living organisms

The structures that all known organisms use to perform these four basic processes are all quite similar, in spite of the odds. All known living things use polymers to perform these four basic functions. Organic chemists have synthesized hundreds of different polymers, yet the only ones used by life, irrespective of species, are polynucleotides, polypeptides, and polysaccharides. Regardless of the species, the DNA, RNA and proteins used in known living systems all have the same chirality, even though there are at least two chemically equivalent choices of chirality for each of these molecules. For example, RNA has four chiral centers in its ribose ring, which means that it has 16 possible stereoisomers—but only one of these stereoisomers is found in the RNA of known living organisms.

Nucleic acids are the genetic material of life

Ten years after the publication of The Origin of Species, nucleic acids were first isolated by Friedrich Miescher in 1869. It took another 75 years after this discovery before DNA was identified as the genetic material of life (Avery et al. 1944). It is quite conceivable that we could have found a different genetic material for each species. In fact, it is still possible that newly identified species might have unknown genetic materials. However, all known life uses the same polymer, polynucleotide (DNA or RNA), for storing species specific information. All known organisms base replication on the duplication of this molecule. The DNA used by living organisms is synthesized using only four nucleosides (deoxyadenosine, deoxythymidine, deoxycytidine, and deoxyguanosine) out of the dozens known (at least 102 occur naturally and many more have been artificially synthesized) (Rozenski et al. 1999; Voet and Voet 1995, p. 969).

Protein catalysis

In order to perform the functions necessary for life, organisms must catalyze chemical reactions. In all known organisms, enzymatic catalysis is based on the abilities provided by protein molecules (and in relatively rare, yet important, cases by RNA molecules). There are over 390 naturally occurring amino acids known (Voet and Voet 1995, p. 69; Garavelli et al. 2001); however, the protein molecules used by all known living organisms are constructed with the same subset of 22 amino acids.

The univeral genetic code

There must be a mechanism for transmitting information from the genetic material to the catalytic material. All known organisms, with extremely rare exceptions, use the same genetic code for this. The few known exceptions are, nevertheless, simple and minor variations from the "universal" genetic code (see Figure 1.1.1) (Lehman 2001; Voet and Voet 1995, p. 967), exactly as predicted by evolutionary biologists based on the theory of common design, years before the genetic code was finally solved (Brenner 1957; Crick et al. 1961; Hinegardner and Engelberg 1963; Judson 1996, p. 280-281).

The scientists who cracked the genetic code in the 1950's and 1960's worked under the assumption that the code was universal or nearly so (Judson 1996, p. 280-281). These scientists (which included Francis Crick, Sydney Brenner, George Gamow, and several others) all made this assumption and justified it based upon teleological reasoning, even in the complete absence of any direct experimental evidence for a universal code.

"Crick urged on his companions two other simplifying assumptions of great audacity. ... they assumed, with some apprehension, that the genetic code would be the same for all living things. There was no evidence whatever for this; .... Yet universality seemed inevitable for an obvious reason: since a mutation that changed even one word or letter of the code would alter most of a creature's proteins, it looked sure to be lethal." (Judson 1996, p. 280-281)

In fact, the assumption of a universal genetic code was instrumental in their success in solving the code. For instance, in 1957, nearly ten years before the genetic code was finally solved, Sydney Brenner published an influential paper in which he concluded that all overlapping triplet codes were impossible if the code was universal (Brenner 1957). This paper was widely considered a landmark work, since many researchers were leaning towards an overlapping code. Of course, it turned out that Brenner was correct about the nature of the true code.

In 1961, five years before the code was deciphered, Crick referenced Brenner's work in his landmark report in the journal Nature, "General nature of the genetic code for proteins" (Crick et al. 1961). Although the organism used in the paper was the bacterium E. coli, Crick titled the paper "the genetic code for proteins", not "a genetic code" or "the genetic code of E. coli". In this paper, Crick and others concluded that the code was (1) a triplet code, (2) non-overlapping, and (3) that the code is read from a fixed starting point (i.e. the "start" codon) (Crick et al. 1961). These conclusions were explicitly based on the assumption that the code was essentially the same in tobacco, humans, and bacteria, though there was no direct empirical support for this assumption. These conclusions, when applied to organisms from bacteria to humans, turned out to be correct. Thus, experimental work also assumed a universal code due to common design.

In fact, in 1963—three years before the code was finally solved—Hinegardner and Engelberg published a paper in Science formally explaining the evolutionary rationale for why the code must be universal (or nearly so) if universal common design were true, since most mutations in the code would likely be lethal to all living things. Note that, although these early researchers predicted a universal genetic code based on common design, they also predicted that minor variations could likely be found. Hinegardner and Engelberg allowed for some variation in the genetic code, and predicted how such variation should be distributed if found:

"... if different codes do exist they should be associated with major taxonomic groups such as phyla or kingdoms that have their roots far in the past." (Hinegardner and Engelberg 1963)

Similarly, before alternate codes were found, Francis Crick and Leslie Orgel expressed surprise that minor variants of the code had not been observed yet: "It is a little surprising that organisms with somewhat different codes do not coexist." (Crick and Orgel 1973, p. 344)

Crick and Orgel were correct in their surprise, and today we know of about a dozen minor variants of the standard, universal genetic code (see the grey, red, and green codons in Figure 1.1.1). As Hinegardner and Engelberg predicted, the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.).

Common metabolism

All known organisms use extremely similar, if not the same, metabolic pathways and metabolic enzymes in processing energy-containing molecules. For example, the fundamental metabolic systems in living organisms are glycolysis, the citric acid cycle, and oxidative phosphorylation. In all eukaryotes and in the majority of prokaryotes, glycolysis is performed in the same ten steps, in the same order, using the same ten enzymes (Voet and Voet 1995, p. 445). In addition, the most basic unit of energy storage, the adenosine triphosphate molecule (ATP), is the same in all species that have been studied.

Potential Falsification:

Thousands of new species are discovered yearly, and new DNA and protein sequences are determined daily from previously unexamined species (Wilson 1992, Ch. 8). At the current rate, which is increasing exponentially, nearly 30,000 new sequences are deposited at GenBank every day, amounting to over 38 million new bases sequenced every day. Each and every one is a test of the theory of common design. When I first wrote these words in 1999, the rate was less than one tenth what it is today (in 2006), and we now have 20 times the amount of DNA sequenced.

Based solely on the theory of common design and the genetics of known organisms, we strongly predict that we will never find any modern species from known phyla on this Earth with a foreign, non-nucleic acid genetic material. We also make the strong prediction that all newly discovered species that belong to the known phyla will use the "standard genetic code" or a close derivative thereof. For example, according to the theory, none of the thousands of new and previously unknown insects that are constantly being discovered in the Brazilian rainforest will have non-nucleic acid genomes. Nor will these yet undiscovered species of insects have genetic codes which are not close derivatives of the standard genetic code. In the absence of the theory of common design, it is quite possible that every species could have a very different genetic code, specific to it only, since there are 1.4 x 1070 informationally equivalent genetic codes, all of which use the same codons and amino acids as the standard genetic code (Yockey 1992). This possibility could be extremely useful for organisms, as it would preclude interspecific viral infections. However, this has not been observed, and the theory of common design effectively prohibits such an observation.

As another example, nine new lemur and two marmoset species (all primates) were discovered in the forests of Madagascar and Brazil in 2000 (Groves 2000; Rasoloarison et al. 2000; Thalmann and Geissmann 2000). Ten new monkey species have been discovered in Brazil alone since 1990 (Van Roosmalen et al. 2000). Nothing in biology prevents these various species from having a hitherto unknown genetic material or a previously unused genetic code—nothing, that is, except for the theory of common design. However, we now know definitively that the new lemurs use DNA with the standard genetic code (Yoder et al. 2000); the marmosets have yet to be tested. Furthermore, each species could use a different polymer for catalysis. The polymers that are used could still be chemically identical yet have different chiralities in different species. There are thousands of thermodynamically equivalent glycolysis pathways (even using the same ten reaction steps but in different orders), so it is possible that every species could have its own specific glycolysis pathway, tailored to its own unique needs. The same reasoning applies to other core metabolic pathways, such as the citric acid cycle and oxidative phosphorylation.

Finally, many molecules besides ATP could serve equally well as the common currency for energy in various species (CTP, TTP, UTP, ITP, or any ATP-like molecule with one of the 293 known amino acids or one of the dozens of other bases replacing the adenosine moiety immediately come to mind). Discovering any new animals or plants that contained any of the anomalous examples proffered above would be potential falsifications of common design , but they have not been found.